3D desktop application with Blender
Currently, I'm developing a web application that allows architects to load their models in a-frame (their models are decimated, processed and texture's are baked). I've been initially using c4d for this but I had a big limitation: I couldn't include python packages (I needed numpy). Then I decided to move to blender and It's working nicely. 

I don't actually know how you could include blender in a .exe or .app file, but since blender it's open source and multi-platform, you should not have big problems. You'll probably have to download the repo from git and do some tweaking.

Since you will have to solve a lot of equations, you could consider using libigl https://libigl.github.io/ 
It's actually a header-only library (in C++ with a python interface) so you could actually use it along with blender, if you want to. I haven't done it, but I'm coding a mesh decimation algorithm with libigl to be include in blender (for academic purpose)

Hope this helped